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1 <tool id="snpSift_geneSets" name="SnpSift GeneSets" version="4.0.0">
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2 <description>Annotating GeneSets, such as Gene Ontology, KEGG, Reactome</description>
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3 <!--
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4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
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5 -->
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6 <expand macro="requirements" />
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7 <macros>
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8 <import>snpSift_macros.xml</import>
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9 </macros>
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10 <command>
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11 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar geneSets -v
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12 #if $db_opts.db_opts_selector == "db"
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13 "${db_opts.database.fields.path}"
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14 #elif $db_opts.db_opts_selector == "histdb"
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15 "$db_opts.histdb"
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16 #end if
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17
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18 $input 2> $log > $output
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19 </command>
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20 <inputs>
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21 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
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22 <conditional name="db_opts">
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23 <param name="db_opts_selector" type="select" label="Select Annotation database" help="">
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24 <option value="db" selected="True">Locally installed database</option>
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25 <option value="histdb">database from your history</option>
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26 </param>
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27 <when value="db">
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28 <param name="database" type="select" label="Molecular Signatures Database (MSigDB)">
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29 <options from_data_table="snpeff_msigdb_database" />
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30 </param>
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31 <param name="histdb" type="hidden" value="" />
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32 </when>
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33 <when value="histdb">
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34 <param name="histdb" type="data" format="txt" label="Molecular Signatures Database (MSigDB)" />
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35 </when>
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36 </conditional>
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37 </inputs>
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38 <outputs>
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39 <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" />
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40 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
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41 </outputs>
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42 <expand macro="stdio" />
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43 <tests>
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44 </tests>
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45 <help>
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46 This tool uses `SnpSift GeneSets`_ to add annotations from `MSigDB`_, a collection of annotated gene sets from different sources including Gene Ontology (GO), KEGG, Reactome.
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47
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48 .. _SnpSift GeneSets: http://snpeff.sourceforge.net/SnpSift.html#geneSets
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49
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50 .. class:: warningmark
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51
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52 The input VCF file must be annotated using SnpEff before performing GeneSets annotations. This is because the tool must know which gene the variant affects.
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53
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54 @EXTERNAL_DOCUMENTATION@
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55
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56 @CITATION_SECTION@
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57
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58 For `MSigDB`_, please cite |Subramanian2005|_.
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59
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60 .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/
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61 .. |Subramanian2005| replace:: Subramanian, A., *et al.* (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. *Proc. Natl. Acad. Sci. U.S.A.* 102(43), 15545-15550
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62 .. _Subramanian2005: http://www.pnas.org/content/102/43/15545
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63 </help>
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64 <expand macro="citations">
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65 <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation -->
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66 </expand>
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67 </tool>
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